Fine Print
R or RStudio command prompt, git, and etc. or crash/burn/blow up your computer, please be aware that I do not accept any responsibility.Important Notes
Git.Bitbucket in a remote public git repository which can be found here.
RStudio using R and R Markdown.
R Markdown as this one.XLConnect, XLConnectJars, and rJava packages.RStudio via R mini BootCamp.Proj file. If this is the case please redo all steps again.R. Please see the instruction below.RStudio. Please see the instruction below.RStudio interactive session by double-clicking the R mini BootCamp.Proj file.
RStudio via R mini BootCamp.Proj file ensures that all of the important paths, user-defined functions and the necessary packages are loaded correctly.RStudio for the first time especially if you are a Windows user or have R version 3.4.3., so please be patient..lastaccessed file in the .checkpoint/YYYY-MM-DD folder unhidden, where YYYY-MM-DD indicates year-month-date. Then restart your RStudio session.R/Settings folder unless you know what you are doing.
R/Settings folder manage the necessary packages for HTML documents and slides as well as the entire workshop.R is the programming software we will use in this BootCamp. It is free and open-source. The necessary installation files can be found here. Please click the link “Download R for (Mac) OS X” and use the appropriate installation package matching your operation system on the files section.RStudio is the integrated development environment (IDE) for R. The free and open-source version of RStudio can be downloaded from here. Note that you should download the RStudio Desktop version not the RStudio Server. At the bottom of that page you will see the installation files. Please use the appropriate link matching your operation system.XQuartz installation is usually required to run some functions in R. Therefore, it is better to install it at the first place.RStudio cheat sheets.R packages are collections of R functions, data, and compiled code in a well-defined format. Packages are the fundamental units of reproducible R code. One of the great things about R is that thousands of packages have been written to solve specific problems in various disciplines. Please see here for all available packages. For packages categorized by areas can be found here. In this page you can search packages by name and find several example codes, details and more. Finally, for recommended packages please see here and here.R coding please see Stack Overflow, Rseek, and google. R Views, R-bloggers, and RPubs are the best places for finding example codes, small tutorials, exploring what others are doing, and even publishing your R code.Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML). For more information about Markdown please see its wiki page.Mou is the markdown editor I use. It is cleans, simple and easy to use. The best parts I like most are it is very fast and it has two-sided view (you can see the preview while writing your markdown).Marked is the other markdown editor I use. I have used it rarely so far since it has a lot of options and tweaks that I need to investigate but unfortunately i don’t have time for that. If you are really into Markdown, I recommend using it.Typora is the markdown editor that I found after a quick search. It seems to be free, have two-sided view, and a lot of other option. It is also available in PC.R Markdown allows you to create documents (PDF, beamer slides, markdown, and HTML) that serve as a neat record of your text and coding with its output (graphs, tables, etc.). R Markdown is a wonderful tool for reproducible research. See here for the details and tutorial of R Markdown. Also, interested users should see here for the range of outputs and formats you can create using R Markdown.R Markdown files, Knitr is necessary which is an engine for dynamic report generation with R. For the details of Knitr see here.R Markdown and Knitr come pre-installed with RStudio so there is need for further action.LaTeX to generate reports in PDF via R Markdown, it is better to install MacTeX distribution.Git is a version control system for tracking changes in computer files. For more information about Git please see its wiki page.Git is mainly used in terminal by Mac users; however, for some users it might be cumbersome (for me as well). Therefore, I suggest you to use a Graphical User Interface (GUI) for Git. All the GUIs can be found here. So far, I have tried SourceTree and GitHub Desktop. I prefer SourceTree since it is has better visualization, simple for beginners and can handle complicated git command very easily for experts. GitHub Desktop might be your choice if you need the simplest GUI.Git. See here and even here for a tutorial of git.Bitbucket or GitHub.R is the programming software we will use in this BootCamp. It is free and open-source. The necessary installation files can be found here. On this page, please click the link “Download R for Windows” and then click “install R for the first time”. Then, the link for the most recent version of R can be found at the top of the page.RStudio is the integrated development environment (IDE) for R. The free and open-source version of RStudio can be downloaded from here. Note that you should download the RStudio Desktop version not the RStudio Server. At the bottom of that page you will see the installation files. Please use the appropriate link matching your operation system.RStudio cheat sheets.R packages are collections of R functions, data, and compiled code in a well-defined format. Packages are the fundamental units of reproducible R code. One of the great things about R is that thousands of packages have been written to solve specific problems in various disciplines. Please see here for all available packages. For packages categorized by areas can be found here. In this page you can search packages by name and find several example codes, details and more. Finally, for recommended packages please see here and here.R coding please see Stack Overflow, Rseek, and google. R Views, R-bloggers, and RPubs are the best places for finding example codes, small tutorials, exploring what others are doing, and even publishing your R code.Markdown is a text-to-HTML conversion tool for web writers. Markdown allows you to write using an easy-to-read, easy-to-write plain text format, then convert it to structurally valid XHTML (or HTML). For more information about Markdown please see its wiki page.Typora is the markdown editor that I found after a quick search. It seems to be free, have two-sided view, and a lot of other option. It is also available in Mac. For PC users, please use the appropriate version matching your operation system, 32 bit or 64 bit.MarkdownPad is the other markdown editor I encountered while searching on Google.R Markdown allows you to create documents (PDF, beamer slides, markdown, and HTML) that serve as a neat record of your text and coding with its output (graphs, tables, etc.). R Markdown is a wonderful tool for reproducible research. See here for the details and tutorial of R Markdown. Also, interested users should see here for the range of outputs and formats you can create using R Markdown.R Markdown files, Knitr is necessary which is an engine for dynamic report generation with R. For the details of Knitr see here.R Markdown and Knitr come pre-installed with RStudio so there is need for further action.LaTeX to generate reports in PDF via R Markdown, it is better to install MacTeX distribution.Git is a version control system for tracking changes in computer files. For more information about Git please see its wiki page.Git is mainly used in command line by PC users; however, for some users it might be cumbersome. Therefore, I suggest you to use a Graphical User Interface (GUI) for Git. All the GUIs can be found here. So far, I have tried SourceTree and GitHub Desktop. I prefer SourceTree since it is has better visualization, simple for beginners and can handle complicated git command very easily for experts. GitHub Desktop might be your choice if you need the simplest GUI.Git. See here and even here for a tutorial of git.Bitbucket or GitHub.R as our main programming software but to make coding easier and more fun we will use RStudio as GUI which will use R at the background. Please take a look at the following screenshots to compare R and RStudio in terms of user functionality.R General View
RStudio General View
My RStudio View
RStudio preferences settings, please see the following screenshots. Note that I am using Mac and the settings might be slightly different for PC users.RStudio preferences.RStudio Prefrences: General
RStudio Prefrences: Code - Editing
RStudio Prefrences: Code - Display
RStudio Prefrences: Code - Saving
RStudio Prefrences: Code - Completion
RStudio Prefrences: Code - Diagnostic
RStudio Prefrences: Appearance
RStudio Prefrences: Pane Layout
RStudio Prefrences: Code - Packages
RStudio Prefrences: R Markdown
RStudio Prefrences: Sweave
RStudio Prefrences: Spelling
RStudio Prefrences: Git/SVN
RStudio Prefrences: Publishing
RStudio Prefrences: Terminal